Sampling
If you want to sample cells to balance well sizes, check this box.

• expList: Indices of wells to sample (comma-separated).
• CellSample: Sampling divisor (e.g., 2 for half, 3 for a third).

Experiments to analyze (without sampling)
Indices for the wells you wish to analyze without sampling.
You can use a comma-separated list (e.g., 0,1,2,3,4,5,6,7,8,9,10,11) or a Python range (e.g., range(0,12)).

Experiment title and number of clusters
Choose a unique title for this run. All output files will use this as a prefix.
Set the number of clusters for k-means analysis.

Feature selection
Check to analyze only kinetics (BPW) or only morphology.
If you wish to run on the entire feature list, leave both unchecked.

Treatments Combination

Specify how your treatments can be combined in your experiments.

• Each treatment name should be 4 characters long.
• Treatments that are not combined with each other should be placed in the same list.
• Treatments that can be combined with others should be in separate lists.

Example:
If your treatments are HGF2, HGF7, DOX1, PHA4, PHA3:

• If HGF2, HGF7, and DOX1 are not combined with each other, put them in the same list: ['HGF2', 'HGF7', 'DOX1']
• If PHA4 and PHA3 are not combined with the others, put them in another list: ['PHA4', 'PHA3']
• The format is: [['HGF2', 'HGF7', 'DOX1'], ['PHA4', 'PHA3']]

You will not find a well named 'HGF2HGF7' or 'HGF2DOX1', but you may find 'HGF7PHA4'.

Note:
If you have a control well (e.g., 'CON'), do not include it in any list.

Single/multiple treatment/control/cell lines

• singleTREAT: True if only one treatment.
• singleCONTROL: True if only one control.
• multipleCL: True if multiple cell lines.

Graph Properties

These settings control the appearance and layout of your output figures. You may need to adjust them depending on your experiment and preferences.

• nrows, ncols:
  Set the number of rows and columns in your experiment figures. For example, if you have 3 cell lines and 8 treatments, use nrows=3 and ncols=8.
  Default: nrows=0, ncols=1

• nColor, nShades:
  Define the number of colors and shades used in the experiment figures.
  Default: nColor=0, nShades=0

• nColorTreat, nShadesTreat:
  Number of colors and shades for treatment-specific figures. Usually, you can leave these at their default values.
  Default: nColorTreat=0, nShadesTreat=0

• nColorLay, nShadesLay:
  Number of colors and shades for y-position (layer) figures.
  Example: nColorLay=3, nShadesLay=3

• figsizeEXP, figsizeTREATS, figsizeCL:
  Set the figure size for experiment, treatment, and cell line figures as (width, height) tuples.
  Example:

  • figsizeEXP = (40, 15)
  • figsizeTREATS = (30, 15)
  • figsizeCL = (15, 5)

Tip: You may need to revisit and adjust these settings to get the best visualization for your data.

Chi-Squared Test Variables

• CON:
  List of control names (comma-separated).
  Example: CON = ['CON'] or CON = ['CON1', 'CON2']

• CL:
  List of cell lines (comma-separated).
  Example: CL = ['BT54', 'MDA2', 'MCF7'] or CL = ['293T']

• wellCON:
  List of well names for controls (one per line, without the 'NNN0' part).
  Example:

  HA033080917CHR1C02BT54CON0WH00
  HA033080917CHR1D02MDA2CON0WH00
  HA033080917CHR1F02MCF7CON0WH00

• controls:
  List of specific experiment names to use as controls (one per line).
  Example:

  BT54HGF7

  Leave blank if not used.

These are the unique experiment names found in your data:

If sampling is enabled, only a subset of cells from selected wells will be used. For example, CellSample=2 means every second cell track is sampled.

The following experiments will be analyzed (excluding sampled experiments if sampling is enabled):

expListT:

The experiment(s) you chose:

AM001100425CHR2B02293TNNIRNOCOWH00

AM001100425CHR2B03293TNNIRNOCOWH00

AM001100425CHR2B04293TNNIRNOCOWH00

AM001100425CHR2C02293TMETRNNIRNOCOWH00

AM001100425CHR2C03293TMETRNNIRNOCOWH00

AM001100425CHR2C04293TMETRNNIRNOCOWH00

AM001100425CHR2D02293TGABYNNIRNOCOWH00

AM001100425CHR2D03293TGABYNNIRNOCOWH00

AM001100425CHR2D04293TGABYNNIRNOCOWH00

AM001100425CHR2E02293TNNIRMETRGABYNOCOWH00

AM001100425CHR2E03293TNNIRMETRGABYNOCOWH00

AM001100425CHR2E04293TNNIRMETRGABYNOCOWH00

The cell line(s):

293T

293T

293T

293T

293T

293T

293T

293T

293T

293T

293T

293T

The treatments are:

Number of features: 49

The Features are:

1. Area

2. Acceleration

3. Acceleration_OLD

4. Acceleration_X

5. Acceleration_Y

6. Coll

7. Coll_CUBE

8. Confinement_Ratio

9. Directional_Change

10. Overall_Displacement

11. Displacement_From_Last_Id

12. Displacement2

13. Ellip_Ax_B_X

14. Ellip_Ax_B_Y

15. Ellip_Ax_C_X

16. Ellip_Ax_C_Y

17. EllipsoidAxisLengthB

18. EllipsoidAxisLengthC

19. Ellipticity_oblate

20. Ellipticity_prolate

21. Instantaneous_Angle

22. Instantaneous_Speed

23. Instantaneous_Speed_OLD

24. Linearity_of_Forward_Progression

25. Mean_Curvilinear_Speed

26. Mean_Straight_Line_Speed

27. Current_MSD_1

28. Final_MSD_1

29. MSD_Linearity_R2_Score

30. MSD_Brownian_Motion_BIC_Score

31. MSD_Brownian_D

32. MSD_Directed_Motion_BIC_Score

33. MSD_Directed_D

34. MSD_Directed_v2

35. Sphericity

36. Total_Track_Displacement

37. Track_Displacement_X

38. Track_Displacement_Y

39. Velocity_X

40. Velocity_Y

41. Eccentricity

42. Min_Distance

43. Velocity_Full_Width_Half_Maximum

44. Velocity_Time_of_Maximum_Height

45. Velocity_Maximum_Height

46. Velocity_Ending_Value

47. Velocity_Ending_Time

48. Velocity_Starting_Value

49. Velocity_Starting_Time

There are 1 significant components

Treatments p-Value

Experiments p-Value AM001100425CHR2B02293TNNIRNOCOWH00

TimeLayers p-Value 0

$\color{blue}{\Large Figure\ 37}$

$\color{blue}{\Large Descriptive\ Table}$

$\color{blue}{\Large Figure\ 38}$

$\color{blue}{\Large ANOVA\ -\ OneWay}$

Could not convert column: Experiment

Could not convert column: Treatments